Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico

Abstract

The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800–1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200–1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.

Ancient DNA Studies in Pre-Columbian Mesoamerica

“…Although RFLPs were reported in earlier studies, the partial or complete sequencing of the mitochondrial Hypervariable Regions 1 and 2 (HVR1 and HVR2, respectively) rapidly became the most common strategy to study mtDNA history. Only a few studies in Mesoamerica have been recently able to reconstruct complete ancient mitogenomes [ 9 , 48 , 49 ] and only one has also generated and analysed genomic data [ 3 ].…”

“…At the time of the Spanish arrival, it was documented that the populations from the Greater Nicoya spoke Mesoamerican-related languages [ 89 ]. In particular, Morales-Arce and colleagues [ 9 ] reconstructed three complete ancient mitogenomes from the Epiclassic-Postclassic archaeological site of Jícaro ( Figure 3 and Table 3 ). Although all of them belonged to the same mitochondrial subhaplogroup (B2d), each individual had a distinct sequence, indicating these individuals were not maternally related in the recent past.…”

The Mitochondrial DNA Landscape of Modern Mexico

“…It covers more than 1.9 million km 2 and is confined by the USA in the North, the Atlantic Ocean in the East, Belize and Guatemala in the South, and the Pacific Ocean in the West. In cultural terms, Mexico is part of Mesoamerica in its center and South and the Greater Southwest and Aridoamerica in its North [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ]. It is generally agreed that the first modern human settlers reached America from Asia via Beringia and colonized the double continent in a rapid southward movement after an incubation period [ 8 , 9 ].…”

“…Mesoamerica had a pivotal role in this process, providing a bridge and geographic bottleneck into South America and continuous interethnic space. Archaeological evidence has shown human presence in today’s Mexico since 12–15 thousand years (ky) [ 5 , 6 , 10 , 11 , 12 ]. The extensive and arid North and the rainy and narrow central and Southern valleys and mountains required different subsistence strategies: while Northern human populations were hunter-gatherers, Indigenous American (also called Native American) groups in South-Central Mexico began to settle in communities following the development of (maize) agriculture from 7–5 ky ago [ 2 , 3 , 5 , 13 , 14 ].…”

Archaeological mitogenomes illuminate the historical ecology of sea otters ( Enhydra lutris ) and the viability of reintroduction

“…Detailed procedures are provided in the electronic supplementary material. In brief, DNA was extracted from dental calculus and dentine using a protocol described in Morales et al [65]. DNA extracts were converted into dual indexed Illumina sequencing libraries and captured using a custom in-solution biotinylated RNA bait set (Arbor Biosciences).…”